Complete mitogenome of the endangered and endemic Nicobar treeshrew (Tupaia nicobarica) and comparison with other Scandentians

Abstract

The Nicobar treeshrew (Tupaia nicobarica) is an endangered small mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate its phylogenetic position with respect to other Scandentians. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (Maximum Likelihood and Bayesian Inference) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (12–19 MYA) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. In the future, whole nuclear genome sequencing is necessary to further improve our understanding of evolutionary relationships among treeshrews, and will have implications for biomedical research.

Mitochondriomics of Clarias Fishes (Siluriformes: Clariidae) with a New Assembly of Clarias camerunensis: Insights into the Genetic Characterization and Diversification

“…The mitogenome of C. camerunensis was AT biased (56.89%), with 32.28% A, 14.87% G, 28.24% C, and 24.61% T. Similar AT biasness of the nucleotide composition was also observed in other Clarias species ranging from 56.89% ( C. camerunensis ) to 58.63% ( C. dussumieri ). A similar pattern of nucleotide composition and AT biasness was observed in other vertebrate mitogenomes described earlier [ 52 , 53 ]. In the C. camerunensis mitogenome, the AT skew and GC skew were 0.135 and −0.310, respectively.…”

The Complete Mitochondrial Genome of Dendrogale murina (Tupaiidae) and Phylogeny of Scandentia

“…The separation time of the Dendrogale genus is estimated as Late Eocene with an average of 35.8 MYA. Due to the use of a younger calibration point at the root [ 38 , 39 ] and the addition of a calibration point to the node B, the common ancestor of Tupaia , Dendrogale , and Ptilocercus genera, we observe an increase in the age of basal nodes within the genus Tupaia compared to the results of Kundu et al [ 26 ]. Our result of dating the divergence of Dendrogale and Tupaia genera is slightly older than shown in Roberts et al [ 11 ], who dated this split approximately to the Eocene–Oligocene boundary based on the analysis of mitochondrial ribosomal genes 12S , tRNA-Val, and 16S .…”

“…Meanwhile, the genetic information and structural motifs of the Dendrogale mitochondrial genome are still unknown. The complete mitochondrial genomes based on phylogenetic reconstruction [ 26 ] analyzed only the Tupaia species and did not include both the basal Scandentia genera Dendrogale and Ptilocercus. To fill this gap of knowledge, the present study first aims to determine the complete mitochondrial genome of Dendrogale murina from Southern Vietnam.…”